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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATATTTGGTCAGTGGGTTGTATCCTTGGAGAAATCATGACAAGGCAACCTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtatgctttatggaaaccttttgagttaaacctactgtctgacattttttttcaattgaatactgtagaacacctttgctgctggtgttatccattacca...

Basic information

species Vitis vinifera
transcript Vv15s0046g02010.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os08g06060.1 (Oryza sativa), 5'ss of exon 4
TGATATTTGGTCAGTGGGTTGTATCCTTGGAGAAATCATGACAAGGCAACCTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtatgctttatggaaaccttttgagttaaacctactgtctgacattttttt--tcaattgaatactgtagaacacctttgctgctggtgttatccattacca---
|||||| ||||| || || || |||||||| || ||| | |||||| | ||| |||||||||| |  |||||||||||||||||||| || || || |||||||| |   |       ||   | || ||  ||||||||    |  | |   |||||    |  |   |   |  ||   |  | || |  ||  ||   |   
TGATATCTGGTCGGTAGGCTGCATCCTTGGTGAGATCGTTACAAGGGAGCCTTTGTTTCCTGGAAAGGATTATGTCCATCAGCTGAGGCTAATAACTGAGgtatgatcactaa-----ttcataattcaagatactgtcttctttgctatcagtcaatcatctgttcatgggaatgttgtttttttgtttgttcttttgttagca

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA16G03670.1 (Glycine max), 5'ss of exon 4
TGATATTTGGTCAGTGGGTTGTATCCTTGGAGAAATCATGACAAGGCAACCTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtat--gctttatggaaaccttttgagttaaacctactgtctgacattttttttcaattga--atactgtagaacacctttgctgctggtgttatccattacca---
|||||| ||||| || ||||| || ||||| |||||||| ||||| ||||| || |||||||||| ||||||||| ||||||||||||||||||||||||||||  |||| ||   || ||  ||| |||   |||   |     ||| | ||   | |||  ||  | | |      | |  | ||  | |  ||  |||  |   
TGATATATGGTCTGTTGGTTGCATACTTGGTGAAATCATAACAAGACAACCGCTCTTTCCTGGCAAAGATTATGTTCATCAGCTGAGACTTATCACAGAGgtattagcttgattccaaactcctgaattag--ctagcata----attatattaagactgattatgttcttgtttgtttgtatttcttttctc-tcttttagaactg

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA07G07270.1 (Glycine max), 5'ss of exon 4
TGATATTTGGTCAGTGGGTTGTATCCTTGGAGAAATCATGACAAGGCAACCTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtat-----gctttatggaaaccttttgagttaaacctactgtctgacattttttttcaattga--atactgtagaacacctttgctgctggtgttatccattacca
|||||| ||||| || ||||| || ||||| |||||||| || || ||||| || |||||||||| ||||||||| ||||||||||||||||||||||||||||     |||| ||   || ||  ||| |||   |||   |     ||| | ||   | |||  ||  | | |      | |  | ||  | |  ||  |||  |
TGATATATGGTCTGTTGGTTGCATACTTGGTGAAATCATAACCAGACAACCACTCTTTCCTGGCAAAGATTATGTTCATCAGCTGAGACTTATCACAGAGgtattattagcttgatttcaaactcctgaattag--ctagcata----attatattaagactgattatgttcttgtttgtttgtatttcttttctc-tcttttagaa

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA09G39190.1 (Glycine max), 5'ss of exon 4
TGATATTTGGTCAGTGGGTTGTATCCTTGGAGAAATCATGACAAGGCAACCTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtatgctttatggaaaccttttgagttaaacctactgtctgacattttt---tttcaattgaatactgtagaacacctttgctgctggtgttatccattacca
|||||||||||| || ||||| |||||||| |||||||| ||||| ||||| || ||||  || | ||||||||| |||||||| || || || || |||||||    ||   | |  |  ||| | | ||||  |   |    ||  |   || |||        | |  ||  | | |  |  | |  |      ||    
TGATATTTGGTCTGTTGGTTGCATCCTTGGTGAAATCATAACAAGACAACCCCTATTTCTGGGGAAAGATTATGTTCATCAGCTCAGGCTGATTACGGAGgtattagctagtcagagatcctgaatgataccttttacatctggttcctgaattgcaagcatgctttctttaattcttctttttatagattagaatgttg---

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT2G46070.1 (Arabidopsis thaliana), 5'ss of exon 4
TGATATTTGGTCAGTGGGTTGTATCCTTGGAGAAATCATGACAAGGCAACCTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtatgctttatggaaaccttttgagttaaacctactgtctgacattttttttcaattgaatactgtagaacacctttgctgctggtgttatccattacca--------
|||||||||||| || || || || || || |||||||||||  | |||||  ||||||| |||| ||||||||| |||||||| || ||||| |||||||||| |   |   ||        |   ||| |  | || | ||| |||| || || ||   | ||   ||  |   |    ||  |  |||||||| |          
TGATATTTGGTCTGTTGGCTGCATACTCGGCGAAATCATGACGGGACAACCGTTGTTTCCAGGCAAAGATTATGTTCATCAGCTTAGGCTTATAACAGAGgtatacc--agtaaagt------aaaaaaagcatcagttttacacttttcttaaactg--caatgcccaattctgatttcact--taatatccatttcttgatattag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|351036505|gb|FQ457218.1|FQ457218
EST:     CTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAG                         CTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
genomic: CTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtatgcttta ... ccttgaaaagCTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
EST: gi|110686022|gb|EE063251.1|EE063251
EST:     CTCTGTTTTCTGGCAGAGAT-ATGTCCATCAGCTGAGACTTATCACAGAG                         CTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGA-GATGATAA
genomic: CTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtatgcttta ... ccttgaaaagCTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAG-TGATAA
EST: gi|351053736|gb|FQ441502.1|FQ441502
EST:     CTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAG                         CTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
genomic: CTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtatgcttta ... ccttgaaaagCTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
EST: gi|110381451|gb|EC934491.1|EC934491
EST:     CTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAG                         CTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
genomic: CTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtatgcttta ... ccttgaaaagCTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
EST: gi|30329963|gb|CD013225.1|CD013225
EST:     GAGACTTATCACAGAG                         CTTATAGGTTCACCTGATGACTCTAGCC-TGGGTTTCTTCGAAGTGATAAT
genomic: GAGACTTATCACAGAGgtatgcttta ... ccttgaaaagCTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
EST: gi|27586442|gb|CB009137.1|CB009137
EST:     CTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAG                         CTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
genomic: CTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtatgcttta ... ccttgaaaagCTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
EST: gi|30134779|gb|CB920117.1|CB920117
EST:     CTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAG                         CTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
genomic: CTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtatgcttta ... ccttgaaaagCTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
EST: gi|351046083|gb|FQ441466.1|FQ441466
EST:     CTCTGGTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAG                         CTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
genomic: CTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtatgcttta ... ccttgaaaagCTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
EST: gi|352786392|gb|FQ479001.1|FQ479001
EST:     CTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAG                         CTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
genomic: CTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtatgcttta ... ccttgaaaagCTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
EST: gi|351039574|gb|FQ461441.1|FQ461441
EST:     CTCTGGTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAG                         CTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT
genomic: CTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtatgcttta ... ccttgaaaagCTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAAT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATATTTGGTCAGTGGGTTGTATCCTTGGAGAAATCATGACAAGGCAACCTCTGTTTCCTGGCAGAGATTATGTCCATCAGCTGAGACTTATCACAGAGgtatgctttatggaaaccttttgagttaaacctactgtctgacattttttttcaattgaatactgtagaacacctttgctgctggtgttatccattacca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atggaaa